2009 Poster Sessions : Sampling Protein Functional Conformations

Student Name : Peggy Yao
Advisor : Jean-Claude Latombe
Research Areas: Artificial Intelligence
Abstract:
Proteins function by interacting with other molecules. Conformational selection theory is becoming more and more popular in explaning how protein-molecule interact. It suggests that a protein presents an ensemble of interchangeable conformations, and the other molecule picks the most favorite one to bind to. Thus, knowing the ensemble of conformations is important in protein function analysis. However, current experimental techniques and computational methods are unable to generate this ensemble efficiently. The challenges of the computational problem is extremely high dimensional space and large number of constraints. Our idea is to eliminate "fake" degrees of freedom by recognizing rigid bodies which are formed due to chemical bonds. In the poster, we will present the framework of our approach, ways of identifying important chemical bonds, conformation sampling algorightm, and some preliminary results.


Bio:
Peggy Yao received the BS degree (with first class honors) major in computer science, minor in biotechnology and the MS degree in computer science from the National University of Singapore. She is a PhD candidate in the
Biomedical Informatics Department, Stanford University. Her research interests include protein 3D structure modeling, computer-aided drug design, and other areas in computational molecular biology.